Branch	Status
master
develop

Table of Contents

• About
• Installation
  • Local Installation
    • Using a Conda Environment
    • Without Conda
• Architecture
• Testing
  • Manual Testing
• Submitting Code

This is the repository for the KBase Narrative Interface. The KBase Narrative Interface builds on the Jupyter Notebook and contains elements to interact with various KBase tools and data stores.

This document contains links to various documentation in the docs directory, with a brief description of each.

If you want to use the KBase Narrative Interface, just point your browser at https://narrative.kbase.us, make a free account, and jump in. This repo is only for people who wish to contribute to the development of the interface.

Short version: Requires the following:

• Python 3.6+
• Anaconda/Miniconda as an environment manager (https://www.anaconda.com/)
• Node.js (latest LTS recommended)
• Bower 1.8.8+

Our git pre-commit hooks allow you to run flake8 and black upon git commit and save you from having to run these linters manually.

• change into the base directory
• pip install pre-commit
• pre-commit install to set up the git hook scripts
• edit a python file and git commit -m <comment> it in to test out the installation

This is the recommended method of installation!

git clone https://github.com/kbase/narrative
cd narrative
conda create -n my_narrative_environment
conda activate my_narrative_environment
./scripts/install_narrative.sh
kbase-narrative

If the previous instructions do not work, try

# source ~/anaconda3/bin/activate or wherever you have python installed
conda create -n my_narrative_environment
conda activate my_narrative_environment
sh scripts/install_narrative.sh
# scripts/install_narrative.sh
kbase-narrative

This process installs lots of requirements of specific versions and may clobber things on your PYTHONPATH.

git clone https://github.com/kbase/narrative
cd narrative
./scripts/install_narrative.sh
kbase-narrative

Long version: Local Narrative setup

In progress!

The Narrative sits on top of the Jupyter Notebook, so most of its architecture is a mirror of that. However, the Narrative's interaction with other KBase elements - namely the data stores and job running services - merits its own description. This will be ongoing (and evolving!), but a brief description of how a job gets run and registered is available here:

Narrative App/Method Running

When deployed in production, the Narrative Interface is compiled into a Docker container. When a user logs in, they have their own instance provisioned for them through an Nginx proxy, which provides a temporary server-side Narrative environment only for that user. Any changes made to a Narrative get saved as part of KBase data stores, but any changes to the file system or the Narrative kernel (e.g. local variables) are lost when the user logs out and their Docker instance gets shut down.

For general testing instructions and guidance refer to docs/testing.md. For information about headless browser testing refer to docs/HeadlessTesting.md.

Follow the gitflow directions located at docs/git-workflow.md to submit code to this repository.